Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( R^REP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( R^FEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSE^REP = 4.28 ± 0.69 versus RMSE^FEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc.     

Halide Anion Triggered Reactions of Michael Acceptors with Tropylium Ion

Tropylium bromide undergoes noncatalyzed, regioselective additions to a large variety of Michael acceptors. In this way, acrylic esters are converted into β‐bromo‐α‐cycloheptatrienylpropionic esters. The reactions are interpreted as nucleophilic attack of bromide ions at the electron‐deficient olefins and the approach of the tropylium ion to the incipient carbanion. Quantum chemical calculations were performed to elucidate the analogy to the amine‐ or phosphine‐catalyzed Rauhut–Currier reactions. Subsequent synthetic transformations of the bromo‐cycloheptatrienylated adducts are reported.     

Acylated flavonoid glycosides from Barringtonia racemosa

Abstract

Using various chromatographic separations, three new acylated flavonoid glycosides, namely barringosides G–I (1–3), were isolated from the water-soluble extract of Barringtonia racemosa branches and leaves. The structure elucidation was performed by extensive analysis of the 1D and 2D NMR and HR-QTOF-MS data. Of the isolated compounds, barringoside I (3) showed moderate inhibitory effects on LPS-induced NO production in RAW264.7 cells with an IC₅₀ of 52.48?±?1.04?µM.     

Triterpene glycosides from the Vietnamese sea cucumber Holothuria edulis

Abstract

From the MeOH extract of the Vietnamese sea cucumber Holothuria edulis, eight triterpene glycosides (1–8), including one new compound namely holothurin A₅ (1), were isolated by using various chromatographic separations. Their structures were established by spectroscopic experiments including 1D, 2D NMR and HR-ESI-MS. Holothurin A₅ (1) has a hydroperoxy group at C-25. To the best of our knowledge, this is the first report of this group in triterpene saponins obtained from sea cucumbers to date. In addition, the in vitro cytotoxicity against five human cancer cell lines (HepG2, KB, LNCaP, MCF7 and SK-Mel2) of all isolated compounds was also evaluated using SRB assays.     

Pullback Attractors for Stochastic Young Differential Delay Equations

We study the asymptotic dynamics of stochastic Young differential delay equations under the regular assumptions on Lipschitz continuity of the coefficient functions. Our main results show that, if there is a linear part in the drift term which has no delay factor and has eigenvalues of negative real parts, then the generated random dynamical system possesses a random pullback attractor provided that the Lipschitz coefficients of the remaining parts are small.

     

Kinetics of the hydrogen abstraction R?OH + H → R?O• + H2 reaction class

This paper presents an application of the reaction class transition state theory (RC‐TST) to predict thermal rate constants for the hydrogen abstraction R? OH + H → R? O^? + H₂ reaction class, where R is an alkyl group. We have derived all parameters for the RC‐TST method for this reaction class from rate constants of 19 representative reactions, coupling with linear energy relationships (LERs) and the barrier height grouping (BHG) approach. Error analyses indicate that the RC‐TST/LER, where only reaction energy is needed, and RC‐TST/BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with satisfactory accuracy for combustion modeling. Specifically for this reaction class, the RC‐TST/LER method has less than 25% systematic errors in the predicted rate constants, whereas the RC‐TST/BHG method has less than 35% error when compared to explicit rate calculations. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 414–429, 2010     

Optical modes in nanoscale one-dimensional spin chains

The spin chain systems with one-dimensional magnetic ordering are promising candidates for quantum optical devices. This paper shows how the optical excitation can induce various phonon modes in an ideal Cu-O chain at various lengths. The calculation was carried out at different level theories including configuration interaction singles for excited states, density functional theory and second-order Möller-Plesset perturbation. In general, the number of modes increases with chain length due to growing asymmetry of atomic positions when chain exceeds 5 nm. There were, however, only two basic modes: one is associated with the symmetric oscillation of oxygen and another with the asymmetric motion of the same along the chain. At the length below 4.3 nm, the Raman activity of the symmetric mode (440 cm⁻¹) dominates. From analysis of density of states, this mode may be associated with the excitation across the lowest LUMO bands with changing in spin state.